filter_file: fix multiple invocations on the same file (#13234)

Since the backup file is only created on the first invocation, it will
contain the original file without any modifications. Further invocations
will then read the backup file, effectively reverting prior invocations.

This can be reproduced easily by trying to install likwid, which will
try to install into /usr/local. Work around this by creating a temporary
file to read from.

lib/spack/llnl/util/filesystem.py

@@ -153,6 +153,7 @@ def groupid_to_group(x):
         tty.debug(msg.format(filename, regex))
 
         backup_filename = filename + "~"
+        tmp_filename = filename + ".spack~"
 
         if ignore_absent and not os.path.exists(filename):
             msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.'
@@ -164,6 +165,10 @@ def groupid_to_group(x):
         if not os.path.exists(backup_filename):
             shutil.copy(filename, backup_filename)
 
+        # Create a temporary file to read from. We cannot use backup_filename
+        # in case filter_file is invoked multiple times on the same file.
+        shutil.copy(filename, tmp_filename)
+
         try:
             extra_kwargs = {}
             if sys.version_info > (3, 0):
@@ -171,7 +176,7 @@ def groupid_to_group(x):
 
             # Open as a text file and filter until the end of the file is
             # reached or we found a marker in the line if it was specified
-            with open(backup_filename, mode='r', **extra_kwargs) as input_file:
+            with open(tmp_filename, mode='r', **extra_kwargs) as input_file:
                 with open(filename, mode='w', **extra_kwargs) as output_file:
                     # Using iter and readline is a workaround needed not to
                     # disable input_file.tell(), which will happen if we call
@@ -190,17 +195,19 @@ def groupid_to_group(x):
             # If we stopped filtering at some point, reopen the file in
             # binary mode and copy verbatim the remaining part
             if current_position and stop_at:
-                with open(backup_filename, mode='rb') as input_file:
+                with open(tmp_filename, mode='rb') as input_file:
                     input_file.seek(current_position)
                     with open(filename, mode='ab') as output_file:
                         output_file.writelines(input_file.readlines())
 
         except BaseException:
+            os.remove(tmp_filename)
             # clean up the original file on failure.
             shutil.move(backup_filename, filename)
             raise
 
         finally:
+            os.remove(tmp_filename)
             if not backup and os.path.exists(backup_filename):
                 os.remove(backup_filename)
 

lib/spack/spack/test/llnl/util/filesystem.py

@@ -362,3 +362,27 @@ def test_filter_files_with_different_encodings(
 
     with open(target_file, mode='r', **extra_kwargs) as f:
         assert replacement in f.read()
+
+
+def test_filter_files_multiple(tmpdir):
+    # All files given as input to this test must satisfy the pre-requisite
+    # that the 'replacement' string is not present in the file initially and
+    # that there's at least one match for the regex
+    original_file = os.path.join(
+        spack.paths.test_path, 'data', 'filter_file', 'x86_cpuid_info.c'
+    )
+    target_file = os.path.join(str(tmpdir), 'x86_cpuid_info.c')
+    shutil.copy(original_file, target_file)
+    # This should not raise exceptions
+    fs.filter_file(r'\<malloc.h\>', '<unistd.h>', target_file)
+    fs.filter_file(r'\<string.h\>', '<unistd.h>', target_file)
+    fs.filter_file(r'\<stdio.h\>',  '<unistd.h>', target_file)
+    # Check the strings have been replaced
+    extra_kwargs = {}
+    if sys.version_info > (3, 0):
+        extra_kwargs = {'errors': 'surrogateescape'}
+
+    with open(target_file, mode='r', **extra_kwargs) as f:
+        assert '<malloc.h>' not in f.read()
+        assert '<string.h>' not in f.read()
+        assert '<stdio.h>' not in f.read()